Wikiomics:RNA-Seq: Difference between revisions
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Darek Kedra (talk | contribs) m (→GMAP/GSNAP) |
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FastA input | FastA and FASTQ input, support for paired ends. | ||
===ERANGE=== | ===ERANGE=== | ||
Revision as of 18:15, 23 November 2010
Mappers
Spliced Mappers (tested)
Tophat
current version: 1.1.4 release 2010.11.16
base mapper: bowtie
SOAPals
http://soap.genomics.org.cn/soapals.html
current version: 1.1 , 05-05-2010
GEM
http://sourceforge.net/apps/mediawiki/gemlibrary/index.php?title=The_GEM_library
current version: GEM-binaries-Linux-x86_64-20100419-003425.tbz2 base mapper: GEM split-mapper
GMAP/GSNAP
http://research-pub.gene.com/gmap/
current version: 2010-07-27
FastA and FASTQ input, support for paired ends.
ERANGE
http://woldlab.caltech.edu/rnaseq/
current version: 3.2.1 from 2010.08.10
base mapper: bowtie or blat
SOLiD data only
(untested)
SplitSeek
http://solidsoftwaretools.com/gf/project/splitseek/
current version: 1.3.2
RNA-mate
http://solidsoftwaretools.com/gf/project/rnamate
current version: 1.01
Spliced Mappers (in developement)
Mapsplice
http://www.netlab.uky.edu/p/bioinfo/MapSplice/
current version: MapSplice 1.14.1 2010.09.30
base mapper: bowtie
SpliceMap
http://www.stanford.edu/group/wonglab/SpliceMap/
current version: 3.3.5.2 2010.10.23
base mapper (preferred): bowtie (others possible) "Currently, only the cannoical GT-AG splice sites are identified."
TAU
http://mocklerlab-tools.cgrb.oregonstate.edu/TAU.html
current version: 1.4 2010.09.06
HMMSplicer
http://derisilab.ucsf.edu/index.php?software=105
current version: 0.9.0 2010.08.30
Developed in Python.
SAW (method no software yet)
Ning K, Fermin D (2010) SAW: A Method to Identify Splicing Events from RNA-Seq Data Based on Splicing Fingerprints. PLoS ONE 5(8): e12047. doi:10.1371/journal.pone.0012047
Spliced Mappers (old)
GMORSE
http://www.genoscope.cns.fr/externe/gmorse/ Proper name: G-Mo.R-Se current version: 06-Nov-2009
It was used for Vitis vinifera genome project.
Not spliced
Mapping short reads to draft genome sequence with multiple contigs poses problems for current spliced mappers.
blat
http://genome.ucsc.edu/FAQ/FAQblat.html
last
Latest: last-139.zip 13-Oct-2010
Installation:
cd src; make
